Category Archives: Genome

Sequencing the Nittany Lion Genome
Help fund our project to sequence the genome of extinct Northeastern mountain lions and discover more about their evolutionary history! Check out our campaign page here: https://pennstate.useed.ne.

By: Maya Evanitsky

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Sequencing the Nittany Lion Genome - Video

By Andrea Rinaldi

An international consortium of public and private partners plans to sequence the genome of wild emmer, an ancestor of modern wheat.

The nutrient-rich wheat could yield ideas to address global hunger by making modern wheat varieties healthier and hardier, scientists from the group say.

Wild emmer is the progenitor of today's durum and bread wheat varieties. It was one of the first crops to be domesticated during the dawn of agriculture, around 10,000 years ago in the Middle East.

"Wild emmer wheat can be naturally crossed with domesticated wheat, hence it is a potential source for wheat improvement," says Assaf Distelfeld, a wheat geneticist at Tel Aviv University, Israel, and lead researcher in the project. Sequencing wild emmer wheat could assist efforts to improve the quality and yields of modern varieties, he says.

For example, wild emmer grain is rich in micronutrients such as iron and zinc. Transferring this trait to bread wheat could reduce malnutrition among people whose diet is based on this staple crop, the scientists say. According to the UN's Food and Agriculture Organization, wheat provides roughly a fifth of the calories eaten around the world.

"In addition, we hope to identify genes that enable wheat to grow better in tough environments, thus improving our food security," says Distelfeld.

But assembling the genome is a complicated task as the wild emmer wheat genome is much more complex than the human one. NRGene, an Israel-based crop sequencing company that will do the work, promises results in six months.

The project partners include Israel's Weizmann Institute of Science, the Sabanci University in Turkey and the Leibniz Institute of Plant Genetics and Crop Plant Research in Germany.

"Researchers from Italy and Australia will soon join the team," says NRGene co-founder Guy Kol. "After project completion, we will make sure that data are freely accessible to all those interested in tapping into the vast emmer wheat genome potential."

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Africa: Wheat Ancestor Sequencing Could Bolster Modern Harvests

Anne Wojcicki, 23andMe co-founder and CEO, speaks onstage during Vanity Fair New Establishment Summit at Yerba Buena Center for the Arts on October 9, 2014 in San Francisco, California. Kimberly White/Getty Images for Vanity Fair

The Human Genome Project, completed in 2003, single-handedly transformed science and medicine. Thanks to DNA sequencing technology we are learning more about human health than ever before, gaining insight into complex diseases and unlocking mysteries about human evolution and ancestry.

Anne Wojcicki, founder and CEO of 23andMe, is one of the pioneers in the booming genomics industry. Wojcicki's company was the first to bring genetic testing to the home frontier with her direct-to-consumer DNA testing kits. While 23andMe has run into its fair share of challenges, the company seeks to empower the public and change the way we think about our health and genetic makeup.

For $99, a 23andMe genetic test promises to reveal ancestral information and raw, unprocessed DNA data. The company says it is also capable of analyzing a person's risk of some 250 conditions and diseases; however, since 2013, the FDA has barred the company from offering DNA tests for health purposes.

CBS News spoke with Wojcicki about how genomics will continue to shape research and medicine. This interview has been condensed and edited.

For those who aren't familiar with your company, can you tell us a little about its purpose?

If you look at our mission statement it's about making sure that the genome is accessible, understandable and that individuals can benefit from the human genome. We fought hard to enable the low-cost, direct-access for a consumer. The next big phase is really about benefiting from the human genome. The reason why we started this company was the research component and the fundamental belief that by really understanding the human genome we will be able to make significant improvements in quality of life, have a novel approach to therapeutics and eventually understand and detect diseases earlier.

Are you continuing to publish your research in major academic journals?

We definitely continue to publish and we will definitely continue to do research. We recognize very clearly that the genome is new and that it's important for us to understand what the impact is on the individual who is getting this data, and how can we actually best deliver that information. That's one thing that we pride ourselves on -- really being experts in understanding how to communicate complicated genetic information.

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23andMe CEO on the future of genomics

OneStart Europe 2015 Semi-finalist: Genome Editing - Harshyaa Makhija
OneStart, co-organised by SR One and the Oxbridge Biotech Roundtable, is the world #39;s largest life science startup accelerator programme. Learn how you can get extended mentoring and win ...

By: OxbridgeBiotech

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OneStart Europe 2015 Semi-finalist: Genome Editing - Harshyaa Makhija - Video

Genome Ver 2 Drum Synth
I spent four minutes with Genome version 2. FREE LOOPS FROM VIDEO http://www.djpuzzle.com/loops/FREE_Genome_DnB_Beats.zip APP LINK http://ipadloops.com/genome-midi-sequencer-ver-2/ Genome...

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Genome Ver 2 Drum Synth - Video

Anuradha Shukla | March 5, 2015

BT for Life Sciences Cloud Compute accelerates genetic analysis.

BT for Life Sciences Cloud Compute has accelerated genetic analysis for Genome Institute of Singapore (GIS).

The institute is focused on revolutionising global healthcare and BT's solution is helping them reach its goal.

Prior to BT, the institute was struggling with vast volumes of information that outstripped available computing resources.

Collaboration between the BT Life Sciences specialist team, GIS and BT Advise Compute resulted in the right BT Cloud Compute architecture to manage the institution's research requirements.

"The real challenge for GIS is no longer the analysis itself, but the vast amount of data produced during analysis that needs to be managed and stored. And this is where the cloud computing resources that BT provides really help us advance the science," said Niranjan Nagarajan, associate director, Computational and Systems Biology Genome Institute of Singapore.

Power of cloud

GIS decided to use the power of the cloud instead of on-premises infrastructure.

Virtual machines effectively scaled computing capacity to address fluctuating data throughput in real time.

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BT processes data for Genome Institute of Singapore

Leveraging whole genome annotation for genotype-phenotype association studies - Eric Boerwinkle
March 10-11, 2015 - From Genome Function to Biomedical Insight: ENCODE and Beyond More: http://www.genome.gov/27560819.

By: GenomeTV

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Leveraging whole genome annotation for genotype-phenotype association studies - Eric Boerwinkle - Video

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Newswise CAMBRIDGE, Mass. (April 3, 2015) By modifying the CRISPR-Cas genome editing system, Whitehead Institute researchers are now able to manipulate Candida albicans genome systematicallyan approach that could help identify novel targets for therapies against this serious pathogen for which there are a limited number of anti-fungal agents.

The ability to engineer Candida albicans with CRISPR technology has changed the playing field, says Whitehead Founding Member Gerald Fink, who is also a professor of biology at MIT. We used to attack this human pathogen with our hands tied behind our back. Our findings cut these bonds, freeing us to forge ahead on problems in basic research and human health.

C. albicans is a commensal organism that normally lives harmlessly on the skin or in the gut. However, this yeast can grow in uncontrolled fashionparticularly in immunocompromised individualscausing fungal infections ranging from mild to lethal. C. albicans is a hardy foe because many strains are resistant to antifungal drugs. To develop new antifungal agents, researchers need to know more about its basic biology.

One tactic for identifying new drug targets in such pathogens is to knock out each of the organisms genes to determine which are essential and therefore appropriate as drug targets. The genome of C. albicans has been particularly difficult to crack because it has two copies of every gene and existing genome editing methods have been inefficient in knocking out both copies simultaneously.

In 2012, a bacterial immunity system the clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated protein 9 (Cas) systemwas repurposed for genome editing. It is precise and efficient enough to edit both copies of a gene in most diploid organisms. However, C. albicans unique genetic makeup renders the standard CRISPR-Cas system ineffective, requiring considerable modification. After extensive efforts, Valmik Vyas, a postdoctoral researcher in Finks lab, engineered a CRISPR system that can work in C. albicans and most other fungi. Vyas describes his system is in this weeks issue of the journal Science Advances.

Using his altered gene editing system in both laboratory and clinical strains, Vyas efficiently mutated in a single experiment both copies of several different genes, including members of a gene family important for antibiotic resistance as well as an essential gene. Vyas estimates that his modified CRISPR-Cas system should be able to target more than 98% of C. albicans genome. That means he should be able to determine which of C. albicans 6000 genes are essential and might make good drug targets.

The improvement efficiency brought by this system expands the scale at which we can do genetics in this important pathogen, says Vyas. Its an exciting time to be working on Candida.

This work is supported by the National Institutes of Health (NIH grant GM035010).

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CRISPR-Cas Genome Editing of Candida albicans Holds Promise for Overcoming Deadly Fungal Infections

CAMBRIDGE, Mass. (April 3, 2015) - By modifying the CRISPR-Cas genome editing system, Whitehead Institute researchers are now able to manipulate Candida albicans' genome systematically--an approach that could help identify novel targets for therapies against this serious pathogen for which there are a limited number of anti-fungal agents.

"The ability to engineer Candida albicans with CRISPR technology has changed the playing field," says Whitehead Founding Member Gerald Fink, who is also a professor of biology at MIT. "We used to attack this human pathogen with our hands tied behind our back. Our findings cut these bonds, freeing us to forge ahead on problems in basic research and human health."

C. albicans is a commensal organism that normally lives harmlessly on the skin or in the gut. However, this yeast can grow in uncontrolled fashion--particularly in immunocompromised individuals--causing fungal infections ranging from mild to lethal. C. albicans is a hardy foe because many strains are resistant to antifungal drugs. To develop new antifungal agents, researchers need to know more about its basic biology.

One tactic for identifying new drug targets in such pathogens is to knock out each of the organism's genes to determine which are essential and therefore appropriate as drug targets. The genome of C. albicans has been particularly difficult to crack because it has two copies of every gene and existing genome editing methods have been inefficient in knocking out both copies simultaneously.

In 2012, a bacterial immunity system --the clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated protein 9 (Cas) system--was repurposed for genome editing. It is precise and efficient enough to edit both copies of a gene in most diploid organisms. However, C. albicans' unique genetic makeup renders the standard CRISPR-Cas system ineffective, requiring considerable modification. After extensive efforts, Valmik Vyas, a postdoctoral researcher in Fink's lab, engineered a CRISPR system that can work in C. albicans and most other fungi. Vyas describes his system is in this week's issue of the journal Science Advances.

Using his altered gene editing system in both laboratory and clinical strains, Vyas efficiently mutated in a single experiment both copies of several different genes, including members of a gene family important for antibiotic resistance as well as an essential gene. Vyas estimates that his modified CRISPR-Cas system should be able to target more than 98% of C. albicans' genome. That means he should be able to determine which of C. albicans' 6000 genes are essential and might make good drug targets.

"The improvement efficiency brought by this system expands the scale at which we can do genetics in this important pathogen," says Vyas. "It's an exciting time to be working on Candida."

###

This work is supported by the National Institutes of Health (NIH grant GM035010).

Gerald Fink's primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a professor of biology at Massachusetts Institute of Technology.

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CRISPR-Cas editing of C. albicans holds promise for overcoming deadly fungal infections

Tuskegee Genome Workshop #39; 15 - What do they say?
Tuskegee University Plant Genome Biotechnology Workshop 2015 - High school teachers and students who participated in the summer event talk about their experience.

By: Channapatna Prakash

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Tuskegee Genome Workshop' 15 - What do they say? - Video